[2023-06-29 20:14:24,091] [INFO] DFAST_QC pipeline started.
[2023-06-29 20:14:24,094] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 20:14:24,094] [INFO] DQC Reference Directory: /var/lib/cwl/stg95c4d202-e2ff-41e2-84e6-26ffe0d903fd/dqc_reference
[2023-06-29 20:14:25,512] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 20:14:25,513] [INFO] Task started: Prodigal
[2023-06-29 20:14:25,513] [INFO] Running command: gunzip -c /var/lib/cwl/stg21e4d05c-d14d-479d-a75e-d1bb30c8a1d4/GCA_021203665.1_ASM2120366v1_genomic.fna.gz | prodigal -d GCA_021203665.1_ASM2120366v1_genomic.fna/cds.fna -a GCA_021203665.1_ASM2120366v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 20:14:29,895] [INFO] Task succeeded: Prodigal
[2023-06-29 20:14:29,895] [INFO] Task started: HMMsearch
[2023-06-29 20:14:29,895] [INFO] Running command: hmmsearch --tblout GCA_021203665.1_ASM2120366v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95c4d202-e2ff-41e2-84e6-26ffe0d903fd/dqc_reference/reference_markers.hmm GCA_021203665.1_ASM2120366v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 20:14:30,163] [INFO] Task succeeded: HMMsearch
[2023-06-29 20:14:30,164] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg21e4d05c-d14d-479d-a75e-d1bb30c8a1d4/GCA_021203665.1_ASM2120366v1_genomic.fna.gz]
[2023-06-29 20:14:30,191] [INFO] Query marker FASTA was written to GCA_021203665.1_ASM2120366v1_genomic.fna/markers.fasta
[2023-06-29 20:14:30,192] [INFO] Task started: Blastn
[2023-06-29 20:14:30,192] [INFO] Running command: blastn -query GCA_021203665.1_ASM2120366v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95c4d202-e2ff-41e2-84e6-26ffe0d903fd/dqc_reference/reference_markers.fasta -out GCA_021203665.1_ASM2120366v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:14:30,857] [INFO] Task succeeded: Blastn
[2023-06-29 20:14:30,861] [INFO] Selected 12 target genomes.
[2023-06-29 20:14:30,861] [INFO] Target genome list was writen to GCA_021203665.1_ASM2120366v1_genomic.fna/target_genomes.txt
[2023-06-29 20:14:30,864] [INFO] Task started: fastANI
[2023-06-29 20:14:30,864] [INFO] Running command: fastANI --query /var/lib/cwl/stg21e4d05c-d14d-479d-a75e-d1bb30c8a1d4/GCA_021203665.1_ASM2120366v1_genomic.fna.gz --refList GCA_021203665.1_ASM2120366v1_genomic.fna/target_genomes.txt --output GCA_021203665.1_ASM2120366v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 20:14:38,862] [INFO] Task succeeded: fastANI
[2023-06-29 20:14:38,862] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95c4d202-e2ff-41e2-84e6-26ffe0d903fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 20:14:38,862] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95c4d202-e2ff-41e2-84e6-26ffe0d903fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 20:14:38,864] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 20:14:38,864] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 20:14:38,864] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-06-29 20:14:38,866] [INFO] DFAST Taxonomy check result was written to GCA_021203665.1_ASM2120366v1_genomic.fna/tc_result.tsv
[2023-06-29 20:14:38,867] [INFO] ===== Taxonomy check completed =====
[2023-06-29 20:14:38,867] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 20:14:38,867] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95c4d202-e2ff-41e2-84e6-26ffe0d903fd/dqc_reference/checkm_data
[2023-06-29 20:14:38,871] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 20:14:38,899] [INFO] Task started: CheckM
[2023-06-29 20:14:38,900] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021203665.1_ASM2120366v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021203665.1_ASM2120366v1_genomic.fna/checkm_input GCA_021203665.1_ASM2120366v1_genomic.fna/checkm_result
[2023-06-29 20:14:59,227] [INFO] Task succeeded: CheckM
[2023-06-29 20:14:59,229] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 20:14:59,251] [INFO] ===== Completeness check finished =====
[2023-06-29 20:14:59,251] [INFO] ===== Start GTDB Search =====
[2023-06-29 20:14:59,252] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021203665.1_ASM2120366v1_genomic.fna/markers.fasta)
[2023-06-29 20:14:59,252] [INFO] Task started: Blastn
[2023-06-29 20:14:59,252] [INFO] Running command: blastn -query GCA_021203665.1_ASM2120366v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95c4d202-e2ff-41e2-84e6-26ffe0d903fd/dqc_reference/reference_markers_gtdb.fasta -out GCA_021203665.1_ASM2120366v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:15:00,231] [INFO] Task succeeded: Blastn
[2023-06-29 20:15:00,236] [INFO] Selected 16 target genomes.
[2023-06-29 20:15:00,236] [INFO] Target genome list was writen to GCA_021203665.1_ASM2120366v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 20:15:00,242] [INFO] Task started: fastANI
[2023-06-29 20:15:00,242] [INFO] Running command: fastANI --query /var/lib/cwl/stg21e4d05c-d14d-479d-a75e-d1bb30c8a1d4/GCA_021203665.1_ASM2120366v1_genomic.fna.gz --refList GCA_021203665.1_ASM2120366v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021203665.1_ASM2120366v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 20:15:06,754] [INFO] Task succeeded: fastANI
[2023-06-29 20:15:06,773] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 20:15:06,773] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_001941225.1	s__CAG-41 sp001941225	93.146	432	602	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA1381;g__CAG-41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585485.1	s__CAG-41 sp910585485	78.7649	162	602	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA1381;g__CAG-41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003460745.1	s__CAG-41 sp900066215	78.1322	178	602	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA1381;g__CAG-41	95.0	97.67	97.16	0.82	0.77	17	-
GCA_010206265.1	s__CAG-41 sp010206265	78.0838	166	602	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA1381;g__CAG-41	95.0	97.79	97.79	0.83	0.83	2	-
GCA_910578235.1	s__CAG-41 sp910578235	77.9855	170	602	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA1381;g__CAG-41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585795.1	s__CAG-41 sp910585795	77.9349	124	602	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA1381;g__CAG-41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579415.1	s__CAG-41 sp910579415	77.8753	134	602	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA1381;g__CAG-41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017406485.1	s__CAG-41 sp017406485	77.8025	106	602	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA1381;g__CAG-41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002438865.1	s__UBA4716 sp002438865	77.3397	67	602	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA1381;g__UBA4716	95.0	99.40	99.40	0.75	0.75	2	-
GCA_018715365.1	s__Ornithomonoglobus_A intestinigallinarum	77.3011	98	602	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA1381;g__Ornithomonoglobus_A	95.0	99.95	99.95	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-06-29 20:15:06,776] [INFO] GTDB search result was written to GCA_021203665.1_ASM2120366v1_genomic.fna/result_gtdb.tsv
[2023-06-29 20:15:06,777] [INFO] ===== GTDB Search completed =====
[2023-06-29 20:15:06,780] [INFO] DFAST_QC result json was written to GCA_021203665.1_ASM2120366v1_genomic.fna/dqc_result.json
[2023-06-29 20:15:06,780] [INFO] DFAST_QC completed!
[2023-06-29 20:15:06,780] [INFO] Total running time: 0h0m43s